net.maizegenetics.pangenome.hapcollapse

Class GVCFTyperPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener

public class GVCFTyperPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Created by zrm22 on 8/1/17.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GVCFTyperPlugin.EMIT_MODE

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
GVCFTyperPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
GVCFTyperPlugin.EMIT_MODE	emitModeParam() Emit Mode for running GVCFTyper.
GVCFTyperPlugin	emitModeParam(GVCFTyperPlugin.EMIT_MODE value) Set Emit_mode.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	inputGVCFDir() Input gvcf directory.
GVCFTyperPlugin	inputGVCFDir(String value) Set Input GVCF Directory.
String	inputIntervalFile() Input interval file to run GVCFTyper with.
GVCFTyperPlugin	inputIntervalFile(String value) Set Input Interval File.
Integer	numThreads() Number of threads for Sentieon to use.
GVCFTyperPlugin	numThreads(Integer value) Set Num Threads.
String	outputVCFDir() Output VCF file directory.
GVCFTyperPlugin	outputVCFDir(String value) Set Output VCF Directory.
String	pluginDescription()
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	referenceFile() Input Reference used to create the gvcf
GVCFTyperPlugin	referenceFile(String value) Set Reference Fasta Sequence.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

GVCFTyperPlugin

public GVCFTyperPlugin(Frame parentFrame,
                       boolean isInteractive)

Method Detail

processData

public net.maizegenetics.plugindef.DataSet processData(net.maizegenetics.plugindef.DataSet input)

Specified by:

processData in interface net.maizegenetics.plugindef.Plugin

Overrides:

processData in class net.maizegenetics.plugindef.AbstractPlugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

pluginDescription

public String pluginDescription()

Specified by:

pluginDescription in interface net.maizegenetics.plugindef.Plugin

Overrides:

pluginDescription in class net.maizegenetics.plugindef.AbstractPlugin

inputGVCFDir

public String inputGVCFDir()

Input gvcf directory.

Returns:

Input GVCF Directory

inputGVCFDir

public GVCFTyperPlugin inputGVCFDir(String value)

Set Input GVCF Directory. Input gvcf directory.

Parameters:

value - Input GVCF Directory

Returns:

this plugin

referenceFile

public String referenceFile()

Input Reference used to create the gvcf

Returns:

Reference Fasta Sequence

referenceFile

public GVCFTyperPlugin referenceFile(String value)

Set Reference Fasta Sequence. Input Reference used to create the gvcf

Parameters:

value - Reference Fasta Sequence

Returns:

this plugin

outputVCFDir

public String outputVCFDir()

Output VCF file directory.

Returns:

Output VCF Directory

outputVCFDir

public GVCFTyperPlugin outputVCFDir(String value)

Set Output VCF Directory. Output VCF file directory.

Parameters:

value - Output VCF Directory

Returns:

this plugin

emitModeParam

public GVCFTyperPlugin.EMIT_MODE emitModeParam()

Emit Mode for running GVCFTyper. Options are all, variant, or confident

Returns:

Emit_mode

emitModeParam

public GVCFTyperPlugin emitModeParam(GVCFTyperPlugin.EMIT_MODE value)

Set Emit_mode. Emit Mode for running GVCFTyper. Options are all, variant, or confident

Parameters:

value - Emit_mode

Returns:

this plugin

inputIntervalFile

public String inputIntervalFile()

Input interval file to run GVCFTyper with.

Returns:

Input Interval File

inputIntervalFile

public GVCFTyperPlugin inputIntervalFile(String value)

Set Input Interval File. Input interval file to run GVCFTyper with.

Parameters:

value - Input Interval File

Returns:

this plugin

numThreads

public Integer numThreads()

Number of threads for Sentieon to use.

Returns:

Num Threads

numThreads

public GVCFTyperPlugin numThreads(Integer value)

Set Num Threads. Number of threads for Sentieon to use.

Parameters:

value - Num Threads

Returns:

this plugin